MPs, backed by the Speaker, are to challenge the expenses watchdog, claiming its rules are forcing them to lay off staff and compromising services to constituents.

The Speaker, John Bercow, is to petition the Independent Parliamentary Standards Authority (Ipsa) over rules which in effect have cut staffing budgets and could force some MPs to live apart from their families. There is anger that Ipsa is refusing to give MPs individual advice, with one MP describing the body as "like a brick wall". Some MPs have renamed Ipsa "I pay sod all" and claim the body, which is independent of parliament, is unaccountable.

The intervention comes amid fresh controversy over MPs' expenses. On Wednesday Eric Illsley, the Labour MP for Barnsley Central, was charged on three counts of false accounting. Next week three former Labour MPs, Jim Devine, Elliot Morley and David Chaytor, will argue in court that they should not face charges because the expenses system is protected by parliamentary privilege.

A letter to the chief executive of Ipsa, Andrew McDonald, organised by the Unite parliamentary staff group, is circulating in the Commons and has been signed by 50 MPs. Such an open revolt will expose MPs to accusations of sour grapes.

McDonald said today that the watchdog's procedures were fair but it would listen to complaints.

Earlier this week, before his re-election as Speaker, Bercow emailed MPs, promising to approach Ipsa on their behalf. "Many colleagues are angry that they are being denied the right of one-to-one advice on the use of the system," he wrote. The complaints include:

• The £110,000 budget for staff is less than some MPs received before, after pensions are taken into account, meaning they have to cut wages, lay off staff or top up the payments themselves. Ipsa said the cap was based on records in the last parliament. It is monitoring the situation and will decide if it needs amending in November.

• No funding was specifically made available to pay maternity leave costs.

• A cap on rent could force some MPs with children to live apart from them during the week.

• Some MPs are struggling with the set-up costs of their new jobs and cannot afford to pay for the flat deposits and new computer equipment for their constituency offices, which have in many cases exceeded the loans on offer. Ipsa is considering options to rectify the problem.

• MPs are complaining that they are getting no proper advice from Ipsa and are being forced to put all inquiries in writing.

Meg Hillier, Labour MP for Hackney South and Shoreditch, said: "It's shocking how badly it has failed to get the arrangements right. I'm urgently seeking written assurances that I'll be able to fulfil my contracts with my staff.It is like dealing with a brick wall." Jim Sheridan, a Labour MP and joint chair of the Unite parliamentary group, said: "Ipsa was rightly designed to hold people to account but they should be efficient as well. It's moved from being about transparency and accountability to seriously affecting our jobs."

The letter was organised jointly by the three staffing groups in the Commons representing members in every party.

McDonald said Ipsa was asking for correspondence in writing "so there is clarity and record about the exchange". He said: "This is a significant change for MPs and for their staff. It's bound to take time to bed in. We are seeking to provide appropriate support to MPs and their staff to help them to make the right decisions within the new rules."